Loki Align - 8 normal small intestine samples

This notebook demonstrates how to run Loki Align on a dataset of 8 adjunction sections of normal small intestine samples. It takes about 3 mins to run the code to align (ST-to-ST and Image-to-ST) each sample (about 20 mins to finish all 7 source samples) on MacBook Pro .

[1]:

import pandas as pd
import matplotlib.pyplot as plt
import os
from matplotlib.colors import rgb2hex

import loki.align
import loki.preprocess
import loki.utils
import loki.plot

/opt/anaconda3/envs/loki/lib/python3.9/site-packages/timm/models/layers/__init__.py:48: FutureWarning: Importing from timm.models.layers is deprecated, please import via timm.layers
  warnings.warn(f"Importing from {__name__} is deprecated, please import via timm.layers", FutureWarning)

We first finetune OmiCLIP model on the target small intestin sample data.

[2]:

%%script echo "Comment this line to fine-tune the model on the target small intestine data."

import subprocess
import open_clip

model_name='coca_ViT-L-14'
pretrained_weight_path='path to the omiclip pretrained weight'
train_csv = 'visium_data/finetune_data.csv'
name = 'finetune_si'

train_command = [
    'python', '-m', 'training.main',
    '--name', name,
    '--save-frequency', '5',
    '--zeroshot-frequency', '10',
    '--report-to', 'wandb',
    '--train-data', train_csv,
    '--csv-img-key', 'img_path',
    '--csv-caption-key', 'label',
    '--warmup', '10',
    '--batch-size', '64',
    '--lr', '5e-6',
    '--wd', '0.1',
    '--epochs', '10',
    '--workers', '16',
    '--model', model_name,
    '--csv-separator', ',',
    '--pretrained', pretrained_weight_path,
    '--lock-text-freeze-layer-norm',
    '--lock-image-freeze-bn-stats',
    '--coca-caption-loss-weight','0',
    '--coca-contrastive-loss-weight','1',
    '--val-frequency', '10',
    '--aug-cfg', 'color_jitter=(0.32, 0.32, 0.32, 0.08)', 'color_jitter_prob=0.5', 'gray_scale_prob=0'
]

subprocess.run(train_command)

Comment this line to fine-tune the model on the target small intestine data.

We provide the embeddings generated from the OmiCLIP model. The sample data and embeddings are stored in the directory data/loki_align/eight_small_intestine_samples, which can be donwloaded from Google Drive link.

Here is a list of the files that are needed to run the cell type decomposition on the pseudo Visium data:

.
├── checkpoint_si
│   ├── V10F24-048_A1_img_features.csv
│   ├── V10F24-048_A1_txt_features.csv
│   ├── V10F24-048_B1_img_features.csv
│   ├── V10F24-048_B1_txt_features.csv
│   ├── V10F24-048_C1_txt_features.csv
│   ├── V10F24-048_C1_img_features.csv
│   ├── V10F24-048_D1_txt_features.csv
│   ├── V10F24-048_D1_img_features.csv
│   ├── V10F24-050_A1_txt_features_zs.csv
│   ├── V10F24-050_A1_img_features.csv
│   ├── V10F24-050_A1_txt_features.csv
│   ├── V10F24-050_B1_img_features.csv
│   ├── V10F24-050_B1_txt_features.csv
│   ├── V10F24-050_C1_txt_features.csv
│   ├── V10F24-050_C1_img_features.csv
│   ├── V10F24-050_D1_txt_features.csv
│   └── V10F24-050_D1_img_features.csv
└── visium_data
    ├── V10F24-048_A1.h5ad
    ├── V10F24-048_B1.h5ad
    ├── V10F24-048_C1.h5ad
    ├── V10F24-048_D1.h5ad
    ├── V10F24-050_A1.h5ad
    ├── V10F24-050_B1.h5ad
    ├── V10F24-050_C1.h5ad
    └── V10F24-050_D1.h5ad

[3]:

data_dir = './data/loki_align/eight_small_intestine_samples/'

[4]:

def get_features(sample_name, feature_name):
    features_path=os.path.join(data_dir, 'checkpoint_si', sample_name+feature_name+'.csv')
    features = pd.read_csv(features_path, index_col=0, header = None)

    return features

[5]:

tar_sample_name = 'V10F24-050_A1'
ad_path = os.path.join(data_dir, 'visium_data', tar_sample_name+'.h5ad')
ad_tar, ad_tar_coor, tar_img = loki.preprocess.prepare_data_for_alignment(ad_path)

Future exception was never retrieved
future: <Future finished exception=BrokenPipeError(32, 'Broken pipe')>
Traceback (most recent call last):
  File "/opt/anaconda3/envs/loki/lib/python3.9/asyncio/unix_events.py", line 665, in write
    n = os.write(self._fileno, data)
BrokenPipeError: [Errno 32] Broken pipe
/opt/anaconda3/envs/loki/lib/python3.9/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")

Loki Align on ST and image alignment

Run tissue alignment using the ST data and image.

Source1

[6]:

src_sample_name = 'V10F24-050_B1'
ad_path = os.path.join(data_dir, 'visium_data', src_sample_name+'.h5ad')
ad_src, ad_src_coor, src_img =  loki.preprocess.prepare_data_for_alignment(ad_path)

/opt/anaconda3/envs/loki/lib/python3.9/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")

Loki Align on ST to ST alignment

Use Loki Align to align ST to ST.

[7]:

tar_features = get_features(tar_sample_name, '_txt_features_zs')
src_features = get_features(src_sample_name, '_txt_features')

[8]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
pca_rgb_comb = (pca_comb_features-pca_comb_features.min(axis=0))/(pca_comb_features.max(axis=0)-pca_comb_features.min(axis=0))
pca_rgb_comb[:,[0,1,2]]=pca_rgb_comb[:,[0,2,1]]
pca_hex_comb = [ rgb2hex(pca_rgb_comb[i,:]) for i in range(pca_rgb_comb.shape[0]) ]

[9]:

plt.figure(figsize=(4,4))
plt.scatter(ad_tar_coor[:,0], ad_tar_coor[:,1], marker='o', s=6, c=pca_hex_comb[:len(tar_features.T)])
plt.title('Target ST')
plt.axis('off')
plt.show()
../_images/notebooks_Loki_Align_case_study_8_small_intestine_14_0.png 
[10]:

cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[11]:

len(pca_hex_comb)

[11]:

6760

[12]:

# loki.plot.plot_alignment_with_img(ad_tar_coor, ad_src_coor, homo_coor, tar_img, src_img, aligned_image, pca_hex_comb, tar_features)

[13]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_18_0.png 
[14]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_19_0.png

Loki Align on image to ST Alignment

Use Loki Align to align image to ST.

[15]:

tar_features = get_features(tar_sample_name, '_txt_features')
src_features = get_features(src_sample_name, '_img_features')

[16]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[17]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_23_0.png 
[18]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_24_0.png

Source2

[19]:

src_sample_name = 'V10F24-050_C1'
ad_path = os.path.join(data_dir, 'visium_data', src_sample_name+'.h5ad')
ad_src, ad_src_coor, src_img =  loki.preprocess.prepare_data_for_alignment(ad_path)

/opt/anaconda3/envs/loki/lib/python3.9/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")

Loki Align on ST to ST alignment

Use Loki Align to align ST to ST.

[20]:

tar_features = get_features(tar_sample_name, '_txt_features_zs')
src_features = get_features(src_sample_name, '_txt_features')

[21]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
pca_rgb_comb = (pca_comb_features-pca_comb_features.min(axis=0))/(pca_comb_features.max(axis=0)-pca_comb_features.min(axis=0))
pca_rgb_comb[:,[0,1,2]]=pca_rgb_comb[:,[0,2,1]]
pca_hex_comb = [ rgb2hex(pca_rgb_comb[i,:]) for i in range(pca_rgb_comb.shape[0]) ]

[22]:

cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[23]:

# loki.plot.plot_alignment_with_img(ad_tar_coor, ad_src_coor, homo_coor, tar_img, src_img, aligned_image, pca_hex_comb, tar_features)

[24]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_32_0.png 
[25]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_33_0.png

Loki Align on image to ST Alignment

Use Loki Align to align image to ST.

[26]:

tar_features = get_features(tar_sample_name, '_txt_features')
src_features = get_features(src_sample_name, '_img_features')

[27]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[28]:

# loki.plot.plot_alignment_with_img(ad_tar_coor, ad_src_coor, homo_coor, tar_img, src_img, aligned_image, pca_hex_comb, tar_features)

[29]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features, boundary_line=False)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_38_0.png 
[30]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_39_0.png

Source3

[31]:

src_sample_name = 'V10F24-050_D1'
ad_path = os.path.join(data_dir, 'visium_data', src_sample_name+'.h5ad')
ad_src, ad_src_coor, src_img =  loki.preprocess.prepare_data_for_alignment(ad_path)

/opt/anaconda3/envs/loki/lib/python3.9/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")

Loki Align on ST to ST alignment

Use Loki Align to align ST to ST.

[32]:

tar_features = get_features(tar_sample_name, '_txt_features_zs')
src_features = get_features(src_sample_name, '_txt_features')

[33]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
pca_rgb_comb = (pca_comb_features-pca_comb_features.min(axis=0))/(pca_comb_features.max(axis=0)-pca_comb_features.min(axis=0))
pca_rgb_comb[:,[0,1,2]]=pca_rgb_comb[:,[0,2,1]]
pca_hex_comb = [ rgb2hex(pca_rgb_comb[i,:]) for i in range(pca_rgb_comb.shape[0]) ]

[34]:

cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[35]:

# loki.plot.plot_alignment_with_img(ad_tar_coor, ad_src_coor, homo_coor, tar_img, src_img, aligned_image, pca_hex_comb, tar_features)

[36]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_47_0.png 
[37]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_48_0.png

Loki Align on image to ST Alignment

Use Loki Align to align image to ST.

[38]:

tar_features = get_features(tar_sample_name, '_txt_features')
src_features = get_features(src_sample_name, '_img_features')

[39]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[40]:

# loki.plot.plot_alignment_with_img(ad_tar_coor, ad_src_coor, homo_coor, tar_img, src_img, aligned_image, pca_hex_comb, tar_features)

[41]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_53_0.png 
[42]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_54_0.png

Source4

[43]:

src_sample_name = 'V10F24-048_C1'
ad_path = os.path.join(data_dir, 'visium_data', src_sample_name+'.h5ad')
ad_src, ad_src_coor, src_img =  loki.preprocess.prepare_data_for_alignment(ad_path)

/opt/anaconda3/envs/loki/lib/python3.9/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")

Loki Align on ST to ST Alignment

Use Loki Align to align ST to ST.

[44]:

tar_features = get_features(tar_sample_name, '_txt_features_zs')
src_features = get_features(src_sample_name, '_txt_features')

[45]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
pca_rgb_comb = (pca_comb_features-pca_comb_features.min(axis=0))/(pca_comb_features.max(axis=0)-pca_comb_features.min(axis=0))
pca_rgb_comb[:,[0,1,2]]=pca_rgb_comb[:,[0,2,1]]
pca_hex_comb = [ rgb2hex(pca_rgb_comb[i,:]) for i in range(pca_rgb_comb.shape[0]) ]

[46]:

cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[47]:

# loki.plot.plot_alignment_with_img(ad_tar_coor, ad_src_coor, homo_coor, tar_img, src_img, aligned_image, pca_hex_comb, tar_features)

[48]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_62_0.png 
[49]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_63_0.png

Loki Align on image to ST Alignment

Use Loki Align to align image to ST.

[50]:

tar_features = get_features(tar_sample_name, '_txt_features')
src_features = get_features(src_sample_name, '_img_features')

[51]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[52]:

# loki.plot.plot_alignment_with_img(ad_tar_coor, ad_src_coor, homo_coor, tar_img, src_img, aligned_image, pca_hex_comb, tar_features)

[53]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_68_0.png 
[54]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_69_0.png

Source5

[55]:

src_sample_name = 'V10F24-048_D1'
ad_path = os.path.join(data_dir, 'visium_data', src_sample_name+'.h5ad')
ad_src, ad_src_coor, src_img =  loki.preprocess.prepare_data_for_alignment(ad_path)

/opt/anaconda3/envs/loki/lib/python3.9/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")

Loki Align on ST to ST alignment

Use Loki Align to align ST to ST.

[56]:

tar_features = get_features(tar_sample_name, '_txt_features_zs')
src_features = get_features(src_sample_name, '_txt_features')

[57]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
pca_rgb_comb = (pca_comb_features-pca_comb_features.min(axis=0))/(pca_comb_features.max(axis=0)-pca_comb_features.min(axis=0))
pca_rgb_comb[:,[0,1,2]]=pca_rgb_comb[:,[0,2,1]]
pca_hex_comb = [ rgb2hex(pca_rgb_comb[i,:]) for i in range(pca_rgb_comb.shape[0]) ]

[58]:

cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[59]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_76_0.png 
[60]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_77_0.png

Loki Align on image to ST Alignment

Use Loki Align to align image to ST.

[61]:

tar_features = get_features(tar_sample_name, '_txt_features')
src_features = get_features(src_sample_name, '_img_features')

[62]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[63]:

# loki.plot.plot_alignment_with_img(ad_tar_coor, ad_src_coor, homo_coor, tar_img, src_img, aligned_image, pca_hex_comb, tar_features)

[64]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_82_0.png 
[65]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_83_0.png

Source6

[66]:

src_sample_name = 'V10F24-048_B1'
ad_path = os.path.join(data_dir, 'visium_data', src_sample_name+'.h5ad')
ad_src, ad_src_coor, src_img =  loki.preprocess.prepare_data_for_alignment(ad_path)

Loki Align on ST to ST alignment

Use Loki Align to align ST to ST.

[67]:

tar_features = get_features(tar_sample_name, '_txt_features_zs')
src_features = get_features(src_sample_name, '_txt_features')

[68]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
pca_rgb_comb = (pca_comb_features-pca_comb_features.min(axis=0))/(pca_comb_features.max(axis=0)-pca_comb_features.min(axis=0))
pca_rgb_comb[:,[0,1,2]]=pca_rgb_comb[:,[0,2,1]]
pca_hex_comb = [ rgb2hex(pca_rgb_comb[i,:]) for i in range(pca_rgb_comb.shape[0]) ]

[69]:

cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[70]:

# loki.plot.plot_alignment_with_img(ad_tar_coor, ad_src_coor, homo_coor, tar_img, src_img, aligned_image, pca_hex_comb, tar_features)

[71]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_91_0.png 
[72]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_92_0.png

Loki Align on image to ST Alignment

Use Loki Align to align image to ST.

[73]:

tar_features = get_features(tar_sample_name, '_txt_features_zs')
src_features = get_features(src_sample_name, '_txt_features')

[74]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[75]:

# loki.plot.plot_alignment_with_img(ad_tar_coor, ad_src_coor, homo_coor, tar_img, src_img, aligned_image, pca_hex_comb, tar_features)

[76]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_97_0.png 
[77]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_98_0.png

Source7

[78]:

src_sample_name = 'V10F24-048_A1'
ad_path = os.path.join(data_dir, 'visium_data', src_sample_name+'.h5ad')
ad_src, ad_src_coor, src_img =  loki.preprocess.prepare_data_for_alignment(ad_path)

Loki Align on ST to ST alignment

Use Loki Align to align ST to ST.

[79]:

tar_features = get_features(tar_sample_name, '_txt_features_zs')
src_features = get_features(src_sample_name, '_txt_features')

[80]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
pca_rgb_comb = (pca_comb_features-pca_comb_features.min(axis=0))/(pca_comb_features.max(axis=0)-pca_comb_features.min(axis=0))
pca_rgb_comb[:,[0,1,2]]=pca_rgb_comb[:,[0,2,1]]
pca_hex_comb = [ rgb2hex(pca_rgb_comb[i,:]) for i in range(pca_rgb_comb.shape[0]) ]

[81]:

cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[82]:

# loki.plot.plot_alignment_with_img(ad_tar_coor, ad_src_coor, homo_coor, tar_img, src_img, aligned_image, pca_hex_comb, tar_features)

[83]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_106_0.png 
[84]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_107_0.png

Loki Align on image to ST Alignment

Use Loki Align to align image to ST.

[85]:

tar_features = get_features(tar_sample_name, '_txt_features_zs')
src_features = get_features(src_sample_name, '_txt_features')

[86]:

pca_comb_features, pca_comb_features_batch = loki.utils.get_pca_by_fit(tar_features, src_features)
cpd_coor, homo_coor, aligned_image = loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img)

[87]:

# loki.plot.plot_alignment_with_img(ad_tar_coor, ad_src_coor, homo_coor, tar_img, src_img, aligned_image, pca_hex_comb, tar_features)

[88]:

loki.plot.plot_alignment(ad_tar_coor, ad_src_coor, homo_coor, pca_hex_comb, tar_features)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_112_0.png 
[89]:

loki.plot.show_image(aligned_image)
../_images/notebooks_Loki_Align_case_study_8_small_intestine_113_0.png 
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